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Epigenetic Study IDs Locus Linked to Unfavorable Phenotype in Cloned Oil Palms

NEW YORK (GenomeWeb) – Muted methylation of the transposon Karma appears to explain the unpredictable, spontaneous production of oil palm clones with undesirable phenotypes such as abnormal fruit shape and low yield, according to a study appearing online today in Nature.

Researchers from Malaysia and the US did an epigenome-wide association study (EWAS) to search for potential culprits in this spontaneous process, known as mantling, in the African oil palm plant Elaeis guineensis

Based on methylation patterns in normal and mantled plants, the team narrowed in on the lone locus involved in mantling and uncovered a characteristic drop in DNA methylation across a long interspersed nuclear element (LINE) retrotransposon locus called Karma in the mantled palms — an epigenetic shift expected to help weed out mantling-prone plantlet clones prior to planting.

"By identifying and culling mantled palms at the nursery stage, one could expect a rapid expansion of the use of clonal palms, and up to a 30 percent increase in yield across relevant planted areas," co-corresponding author Ravigadevi Sambanthamurthi, director of the Malaysian Palm Oil Board's Advanced Breeding and Biotechnology Centre, said in a statement.

Tissue culture methods for palm oil plants have been available for decades, the researchers explained. But the approach has been underused due to the presence of so-called somaclonal variants — particularly mantled clones — that turn up unpredictably in genetically identical palm oil plants.

"Typically, palms that are propagated through tissue culture are clones of the best hybrid trees with yields that are 20 to 30 percent higher than trees propagated through seeds," Sambanthamurthi explained. "But the threat of mantling has severely limited the cultivation of clonal palms to approximately one percent of land committed to oil palm."

In an effort to find epigenetic contributors to this process, Sambanthamurthi and colleagues performed an EWAS that relied on genome and transcriptome sequences for African (E. guineensis) and South American (E. oleifera) oil palm plants, first sequenced in 2013.

Using custom Roche NimbleGen arrays, the team profiled cytosine methylation patterns across the genomes of 54 normal and 43 mantled E. guineensis oil palm clones, along with 10 of the parental hybrid palms from which the clones were generated.

Among the genome regions that were differentially methylated in parental plants and their clones, the researchers found that mantling tended to coincide with a dip in methylation, particularly across transposons and other repeat sequences.

But just one locus was consistently methylated at lower levels in the mantled clones: a chromosome 12 site in and around oil palm transcription factor genes that contains a newly detected LINE element.

Given the similarities between this LINE element and a related rice retrotransposon called Karma, the team dubbed the mantle-associated version the epiallele 'Bad Karma' and the normal fruit set epiallele 'Good Karma.' 

After verifying this association through whole-genome and targeted bisulfite sequencing, as well as quantitative PCR testing, the researchers demonstrated that the Bad Karma epiallele contributes to mantling by interfering with messenger RNA splicing in ways that produce truncated forms of a transcription factor involved in flowering.